The Theoretical Study on a Nano Biosystem Consisting of Nano Tube-Catalytic Site of Bacillus Subtilis α-Amylase, PDB: 1UA7

Document Type : Research Paper


Department of Biology, Payamnoor University, Qom, I. R. Iran


α-Amylase has been studied extensively from various sides. This enzyme is used in many industries .Many applications of this enzyme have encouraged us for greater attempts on the study of α-amylase and to search for more effective processes. In this investigation, the structure of nanotube - catalytic site of bacillus subtilis α- amylase was optimized by hyperchem 7.0 and then it was investigated with ab initio/hartree fock and density functional theory /B3LYP methods using the STO-3G, 3-21G and 6-31G basis sets for a physicochemical explanation of interactions within these nano biosystem. Then nuclear Magnetic Resonance (NMR) parameters and so charge, dipole moment, and stability energy were calculated on the optimized structure. We have found each of active atoms that indeed play an important role in imparting extra stability. In the current study, we have reported the NMR parameters of 8 atoms of catalytic site of bacillus subtilis alpha-amylasethe. Interesting finding of the present study is that in NMR shielding for each of active atoms, O8 and O14 had maximal shift in all of levels. In catalytic mechanism of this enzyme, O14 is adopting a chair structure leading to the easy cleavage of the glucoside bond (fixer for catalysis). This investigation suggests that nanotube interactions in this nano biosystems indeed play an important role in imparting extra stability of the catalytic site of the enzyme .Energy parameters in B3LYP level in different basis sets have more negative values than HF and have indicated the most stability in B3LYP6-31/G level and so dipole moment in this structure have observed that in HF3-21/G is maximum. The aim of this work was to discuss the aspects of the electronic structure of this nano biosystem to increase their advantages in practical applications.